Contacts of the strand formed by residues 113 - 117 (chain V) in PDB entry 3EXG
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with VAL 113 (chain V).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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76V PRO 3.2 11.2 + - - +
77V ILE* 3.5 10.3 - - + -
78V CYS* 2.8 29.3 + - - +
112V ILE* 1.3 85.7 - - - +
114V PHE* 1.3 72.9 + - - +
115V ARG* 3.8 10.7 + - + -
157V ILE* 4.4 6.1 - - + -
160V ALA* 3.2 40.8 - - + +
161V ILE* 3.8 7.2 - - + +
167V VAL* 3.4 11.2 - - + +
169V VAL* 4.1 16.8 - - + -
1004V K 3.4 4.3 - - - -
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Residues in contact with PHE 114 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63V ALA* 4.4 9.4 - - + -
67V VAL* 4.1 13.2 - - + -
78V CYS* 3.5 23.8 - - + -
80V PHE* 3.8 31.2 - + + -
83V PHE* 4.1 10.5 - - + -
93V VAL* 3.6 44.2 - - + -
97V ALA* 4.7 4.3 - - + -
112V ILE* 3.4 44.4 - - + -
113V VAL* 1.3 74.6 - - - +
115V ARG* 1.3 61.7 + - - +
166V PRO* 4.8 3.4 - - + -
167V VAL 2.9 14.8 + - - +
168V VAL* 3.3 10.0 - - + -
169V VAL* 2.7 26.2 + - - +
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Residues in contact with ARG 115 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9V ILE* 4.6 1.3 - - - +
13V MET* 3.6 29.1 - - - +
25V LEU* 4.2 5.3 - - - +
39V VAL* 4.0 16.9 - - - +
77V ILE* 3.8 23.6 - - + -
78V CYS 3.1 6.2 + - - +
79V GLU* 3.4 48.3 + - + +
80V PHE* 2.9 26.7 + - - +
83V PHE* 4.0 6.3 - - - -
113V VAL* 4.4 2.9 - - + -
114V PHE* 1.3 77.0 - - - +
116V GLY* 1.3 59.3 + - - +
157V ILE* 3.6 21.1 - - - -
169V VAL* 3.4 24.2 - - + +
171V GLU* 2.6 43.9 + - - +
176V TYR* 3.9 5.1 + - - -
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Residues in contact with GLY 116 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79V GLU* 4.5 0.4 - - - -
80V PHE 3.5 8.7 - - - -
83V PHE* 3.6 11.8 - - - -
115V ARG* 1.3 82.7 - - - +
117V PRO* 1.3 75.5 - - - +
169V VAL 3.5 4.7 + - - +
171V GLU* 3.0 35.3 + - - -
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Residues in contact with PRO 117 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37V TYR* 3.8 17.7 - - + -
79V GLU* 5.1 2.7 - - - +
80V PHE 3.6 3.6 - - - +
81V MET 3.0 29.4 - - - +
82V THR* 3.3 10.3 - - + -
83V PHE* 2.8 30.5 + - - +
115V ARG* 5.4 0.4 - - - +
116V GLY* 1.3 85.1 - - - +
118V ASN* 1.3 55.4 + - - +
171V GLU* 3.1 10.5 - - + +
173V GLU* 3.6 30.1 - - + +
176V TYR* 3.6 17.2 - - + +
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il